tests/testthat/test_010_orgdb_tritrypdb.R

In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

start <- as.POSIXlt(Sys.time())
library(testthat)
library(EuPathDB)
context("020_orgdb_tritrypdb
  12\n")

## These tests are intended to ensure that the creation of new orgdbs are sane.
## Since I am primarily interested in the tritrypdb, I will focus there.

webservice <- "tritrypdb"
wanted <- "Friedlin"
meta <- download_eupath_metadata(overwrite=FALSE, webservice=webservice)
all_metadata <- meta[["valid"]]
eu_version <- get_versions()[["eu_version"]]

entry <- get_eupath_entry(species=wanted, metadata=all_metadata)
orgdb_result <- make_eupath_orgdb(entry, copy_s3=TRUE, verbose=TRUE)
expected <- paste0("org.Lmajor.Friedlin.", eu_version, ".eg.db")
actual <- as.character(orgdb_result)
test_that("Did make_eupath_orgdb return an expected result?", {
  expect_equal(actual, expected)
})
library(expected, character.only=TRUE)
orgdb_annot <- load_eupath_annotations(entry)
test_that("Do we get some expected annotation data?", {
  expect_gt(ncol(orgdb_annot), 100)
  expect_gt(nrow(orgdb_annot), 9400)
})
orgdb_go <- load_eupath_go(entry)
test_that("Do we get some expected GO data?", {
  expect_equal(ncol(orgdb_go), 4)
  expect_gt(nrow(orgdb_go), 35800)
})

wanted <- "panamensis MHOM/COL"
entry <- get_eupath_entry(species=wanted, metadata=meta)
orgdb_result <- make_eupath_orgdb(entry, copy_s3=TRUE, verbose=TRUE)
expected <- paste0("org.Lpanamensis.MHOMCOL81L13.", eu_version, ".eg.db")
actual <- as.character(orgdb_result)
test_that("Did make_eupath_orgdb return an expected result?", {
  expect_equal(actual, expected)
})
library(expected, character.only=TRUE)
orgdb_annot <- load_eupath_annotations(entry)
test_that("Do we get some expected annotation data?", {
  expect_gt(ncol(orgdb_annot), 100)
  expect_gt(nrow(orgdb_annot), 8700)
})
orgdb_go <- load_eupath_go(entry)
test_that("Do we get some expected GO data?", {
  expect_equal(ncol(orgdb_go), 4)
  expect_gt(nrow(orgdb_go), 19600)
})

end <- as.POSIXlt(Sys.time())
elapsed <- round(x=as.numeric(end) - as.numeric(start))
message(paste0("\nFinished 020_orgdb_tritrypdb in ", elapsed,  " seconds."))